DWIBiasCorrect brick¶
Perform B1 field inhomogeneity correction for a DWI image¶
(mrtrix dwibiascorrect command)
Please note that, in mia_processes, MRtrix bricks required diffusion data in MRtrix .mif format. The MRConvert brick could be used to convert diffusion data in NIfTI format into MRtrix .mif format. In this case, bvec and bval file should be specified.
Mandatory inputs parameters:
- in_file (a string representing an existing file)
Input DWI image (valid extensions: [.mif]).
ex. '/home/username/data/raw_data/DWI.mif'
Optional inputs with default value parameters:
- use_fsl (a boolean, default value is False, optional)
Use FSL FAST to estimate the inhomogeneity field. FSL should be configured in populse.
ex. False
- use_ans (a boolean, default value is True, optional)
Use ANTS N4 to estimate the inhomogeneity field. ANTS should be configured in populse.
ex. True
Optional inputs parameters:
- in_mask (a string representing an existing file, optional)
Input mask image for bias field estimation (valid extensions: [.mif, .nii, .nii.gz]).
ex. '/home/username/data/derived_data/DWI_brainmask.nii'
Outputs parameters:
- out_file (a pathlike object or string representing a file)
The output bias corrected DWI image
ex. '/home/username/data/derived_data/DWI_unbias.mif'
- bias_field_map (a pathlike object or string representing a file)
The output bias field map
ex. '/home/username/data/derived_data/DWI_bias_field_map.mif'
Useful links: